[query] Remove BlockMatrix persist from Backend interface

hail/src/main/scala/is/hail/backend/Backend.scala

@@ -12,11 +12,10 @@ import is.hail.io.{BufferSpec, TypedCodecSpec}
 import is.hail.io.fs._
 import is.hail.io.plink.LoadPlink
 import is.hail.io.vcf.LoadVCF
-import is.hail.linalg.BlockMatrix
 import is.hail.types._
 import is.hail.types.encoded.EType
 import is.hail.types.physical.PTuple
-import is.hail.types.virtual.{BlockMatrixType, TFloat64}
+import is.hail.types.virtual.TFloat64
 import is.hail.utils._
 import is.hail.variant.ReferenceGenome
 
@@ -77,15 +76,6 @@ abstract class Backend extends Closeable {
 
   def broadcast[T: ClassTag](value: T): BroadcastValue[T]
 
-  def persist(backendContext: BackendContext, id: String, value: BlockMatrix, storageLevel: String)
-    : Unit
-
-  def unpersist(backendContext: BackendContext, id: String): Unit
-
-  def getPersistedBlockMatrix(backendContext: BackendContext, id: String): BlockMatrix
-
-  def getPersistedBlockMatrixType(backendContext: BackendContext, id: String): BlockMatrixType
-
   def parallelizeAndComputeWithIndex(
     backendContext: BackendContext,
     fs: FS,

hail/src/main/scala/is/hail/backend/ExecuteContext.scala

@@ -6,6 +6,7 @@ import is.hail.asm4s.HailClassLoader
 import is.hail.backend.local.LocalTaskContext
 import is.hail.expr.ir.lowering.IrMetadata
 import is.hail.io.fs.FS
+import is.hail.linalg.BlockMatrix
 import is.hail.utils._
 import is.hail.variant.ReferenceGenome
 
@@ -71,6 +72,7 @@ object ExecuteContext {
     flags: HailFeatureFlags,
     backendContext: BackendContext,
     irMetadata: IrMetadata,
+    blockMatrixCache: mutable.Map[String, BlockMatrix],
   )(
     f: ExecuteContext => T
   ): T = {
@@ -89,6 +91,7 @@ object ExecuteContext {
           flags,
           backendContext,
           irMetadata,
+          blockMatrixCache,
         ))(f(_))
       }
     }
@@ -118,6 +121,7 @@ class ExecuteContext(
   val flags: HailFeatureFlags,
   val backendContext: BackendContext,
   val irMetadata: IrMetadata,
+  val BlockMatrixCache: mutable.Map[String, BlockMatrix],
 ) extends Closeable {
 
   val rngNonce: Long =
@@ -184,6 +188,7 @@ class ExecuteContext(
     flags: HailFeatureFlags = this.flags,
     backendContext: BackendContext = this.backendContext,
     irMetadata: IrMetadata = this.irMetadata,
+    blockMatrixCache: mutable.Map[String, BlockMatrix] = this.BlockMatrixCache,
   )(
     f: ExecuteContext => A
   ): A =
@@ -200,5 +205,6 @@ class ExecuteContext(
       flags,
       backendContext,
       irMetadata,
+      blockMatrixCache,
     ))(f)
 }

hail/src/main/scala/is/hail/backend/caching/BlockMatrixCache.scala

@@ -0,0 +1,33 @@
+package is.hail.backend.caching
+
+import is.hail.linalg.BlockMatrix
+
+import scala.collection.mutable
+
+class BlockMatrixCache extends mutable.AbstractMap[String, BlockMatrix] with AutoCloseable {
+
+  private[this] val blockmatrices: mutable.Map[String, BlockMatrix] =
+    mutable.LinkedHashMap.empty
+
+  override def +=(kv: (String, BlockMatrix)): BlockMatrixCache.this.type = {
+    blockmatrices += kv; this
+  }
+
+  override def -=(key: String): BlockMatrixCache.this.type = {
+    get(key).foreach { bm => bm.unpersist(); blockmatrices -= key }; this
+  }
+
+  override def get(key: String): Option[BlockMatrix] =
+    blockmatrices.get(key)
+
+  override def iterator: Iterator[(String, BlockMatrix)] =
+    blockmatrices.iterator
+
+  override def clear(): Unit = {
+    blockmatrices.values.foreach(_.unpersist())
+    blockmatrices.clear()
+  }
+
+  override def close(): Unit =
+    clear()
+}

hail/src/main/scala/is/hail/backend/local/LocalBackend.scala

@@ -10,11 +10,10 @@ import is.hail.expr.ir._
 import is.hail.expr.ir.analyses.SemanticHash
 import is.hail.expr.ir.lowering._
 import is.hail.io.fs._
-import is.hail.linalg.BlockMatrix
 import is.hail.types._
 import is.hail.types.physical.PTuple
 import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
-import is.hail.types.virtual.{BlockMatrixType, TVoid}
+import is.hail.types.virtual.TVoid
 import is.hail.utils._
 import is.hail.variant.ReferenceGenome
 
@@ -113,6 +112,7 @@ class LocalBackend(
             ExecutionCache.fromFlags(flags, fs, tmpdir)
         },
         new IrMetadata(),
+        ImmutableMap.empty,
       )(f)
     }
 
@@ -215,15 +215,6 @@ class LocalBackend(
   ): TableReader =
     LowerDistributedSort.distributedSort(ctx, stage, sortFields, rt, nPartitions)
 
-  def persist(backendContext: BackendContext, id: String, value: BlockMatrix, storageLevel: String)
-    : Unit = ???
-
-  def unpersist(backendContext: BackendContext, id: String): Unit = ???
-
-  def getPersistedBlockMatrix(backendContext: BackendContext, id: String): BlockMatrix = ???
-
-  def getPersistedBlockMatrixType(backendContext: BackendContext, id: String): BlockMatrixType = ???
-
   def tableToTableStage(ctx: ExecuteContext, inputIR: TableIR, analyses: LoweringAnalyses)
     : TableStage =
     LowerTableIR.applyTable(inputIR, DArrayLowering.All, ctx, analyses)

hail/src/main/scala/is/hail/backend/service/ServiceBackend.scala

@@ -14,7 +14,6 @@ import is.hail.expr.ir.functions.IRFunctionRegistry
 import is.hail.expr.ir.lowering._
 import is.hail.io.fs._
 import is.hail.io.reference.{IndexedFastaSequenceFile, LiftOver}
-import is.hail.linalg.BlockMatrix
 import is.hail.services.{BatchClient, JobGroupRequest, _}
 import is.hail.services.JobGroupStates.{Cancelled, Failure, Running, Success}
 import is.hail.types._
@@ -375,15 +374,6 @@ class ServiceBackend(
   ): TableReader =
     LowerDistributedSort.distributedSort(ctx, inputStage, sortFields, rt, nPartitions)
 
-  def persist(backendContext: BackendContext, id: String, value: BlockMatrix, storageLevel: String)
-    : Unit = ???
-
-  def unpersist(backendContext: BackendContext, id: String): Unit = ???
-
-  def getPersistedBlockMatrix(backendContext: BackendContext, id: String): BlockMatrix = ???
-
-  def getPersistedBlockMatrixType(backendContext: BackendContext, id: String): BlockMatrixType = ???
-
   def tableToTableStage(ctx: ExecuteContext, inputIR: TableIR, analyses: LoweringAnalyses)
     : TableStage =
     LowerTableIR.applyTable(inputIR, DArrayLowering.All, ctx, analyses)
@@ -402,6 +392,7 @@ class ServiceBackend(
         flags,
         serviceBackendContext,
         new IrMetadata(),
+        ImmutableMap.empty,
       )(f)
     }
 

hail/src/main/scala/is/hail/backend/spark/SparkBackend.scala

@@ -4,14 +4,14 @@ import is.hail.{HailContext, HailFeatureFlags}
 import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend._
+import is.hail.backend.caching.BlockMatrixCache
 import is.hail.backend.py4j.Py4JBackendExtensions
 import is.hail.expr.Validate
 import is.hail.expr.ir._
 import is.hail.expr.ir.analyses.SemanticHash
 import is.hail.expr.ir.lowering._
 import is.hail.io.{BufferSpec, TypedCodecSpec}
 import is.hail.io.fs._
-import is.hail.linalg.BlockMatrix
 import is.hail.rvd.RVD
 import is.hail.types._
 import is.hail.types.physical.{PStruct, PTuple}
@@ -351,20 +351,8 @@ class SparkBackend(
   override val longLifeTempFileManager: TempFileManager =
     new OwningTempFileManager(fs)
 
-  val bmCache: SparkBlockMatrixCache = SparkBlockMatrixCache()
-
-  def persist(backendContext: BackendContext, id: String, value: BlockMatrix, storageLevel: String)
-    : Unit = bmCache.persistBlockMatrix(id, value, storageLevel)
-
-  def unpersist(backendContext: BackendContext, id: String): Unit = unpersist(id)
-
-  def getPersistedBlockMatrix(backendContext: BackendContext, id: String): BlockMatrix =
-    bmCache.getPersistedBlockMatrix(id)
-
-  def getPersistedBlockMatrixType(backendContext: BackendContext, id: String): BlockMatrixType =
-    bmCache.getPersistedBlockMatrixType(id)
-
-  def unpersist(id: String): Unit = bmCache.unpersistBlockMatrix(id)
+  private[this] val bmCache: BlockMatrixCache =
+    new BlockMatrixCache()
 
   def createExecuteContextForTests(
     timer: ExecutionTimer,
@@ -387,6 +375,7 @@ class SparkBackend(
           ExecutionCache.forTesting
       },
       new IrMetadata(),
+      ImmutableMap.empty,
     )
 
   override def withExecuteContext[T](f: ExecuteContext => T)(implicit E: Enclosing): T =
@@ -406,6 +395,7 @@ class SparkBackend(
             ExecutionCache.fromFlags(flags, fs, tmpdir)
         },
         new IrMetadata(),
+        bmCache,
       )(f)
     }
 
@@ -470,6 +460,7 @@ class SparkBackend(
   override def asSpark(op: String): SparkBackend = this
 
   def close(): Unit = {
+    bmCache.close()
     SparkBackend.stop()
     longLifeTempFileManager.close()
   }

hail/src/main/scala/is/hail/expr/ir/BlockMatrixIR.scala

@@ -1,8 +1,7 @@
 package is.hail.expr.ir
 
-import is.hail.HailContext
 import is.hail.annotations.NDArray
-import is.hail.backend.{BackendContext, ExecuteContext}
+import is.hail.backend.ExecuteContext
 import is.hail.expr.Nat
 import is.hail.expr.ir.lowering.{BMSContexts, BlockMatrixStage2, LowererUnsupportedOperation}
 import is.hail.io.{StreamBufferSpec, TypedCodecSpec}
@@ -106,7 +105,7 @@ object BlockMatrixReader {
   def fromJValue(ctx: ExecuteContext, jv: JValue): BlockMatrixReader =
     (jv \ "name").extract[String] match {
       case "BlockMatrixNativeReader" => BlockMatrixNativeReader.fromJValue(ctx.fs, jv)
-      case "BlockMatrixPersistReader" => BlockMatrixPersistReader.fromJValue(ctx.backendContext, jv)
+      case "BlockMatrixPersistReader" => BlockMatrixPersistReader.fromJValue(ctx, jv)
       case _ => jv.extract[BlockMatrixReader]
     }
 }
@@ -274,22 +273,20 @@ case class BlockMatrixBinaryReader(path: String, shape: IndexedSeq[Long], blockS
 case class BlockMatrixNativePersistParameters(id: String)
 
 object BlockMatrixPersistReader {
-  def fromJValue(ctx: BackendContext, jv: JValue): BlockMatrixPersistReader = {
+  def fromJValue(ctx: ExecuteContext, jv: JValue): BlockMatrixPersistReader = {
     implicit val formats: Formats = BlockMatrixReader.formats
     val params = jv.extract[BlockMatrixNativePersistParameters]
     BlockMatrixPersistReader(
       params.id,
-      HailContext.backend.getPersistedBlockMatrixType(ctx, params.id),
+      BlockMatrixType.fromBlockMatrix(ctx.BlockMatrixCache(params.id)),
     )
   }
 }
 
 case class BlockMatrixPersistReader(id: String, typ: BlockMatrixType) extends BlockMatrixReader {
   def pathsUsed: Seq[String] = FastSeq()
   lazy val fullType: BlockMatrixType = typ
-
-  def apply(ctx: ExecuteContext): BlockMatrix =
-    HailContext.backend.getPersistedBlockMatrix(ctx.backendContext, id)
+  def apply(ctx: ExecuteContext): BlockMatrix = ctx.BlockMatrixCache(id)
 }
 
 case class BlockMatrixMap(child: BlockMatrixIR, eltName: Name, f: IR, needsDense: Boolean)

hail/src/main/scala/is/hail/expr/ir/BlockMatrixWriter.scala

@@ -1,6 +1,5 @@
 package is.hail.expr.ir
 
-import is.hail.HailContext
 import is.hail.annotations.Region
 import is.hail.asm4s._
 import is.hail.backend.ExecuteContext
@@ -190,7 +189,7 @@ case class BlockMatrixPersistWriter(id: String, storageLevel: String) extends Bl
   def pathOpt: Option[String] = None
 
   def apply(ctx: ExecuteContext, bm: BlockMatrix): Unit =
-    HailContext.backend.persist(ctx.backendContext, id, bm, storageLevel)
+    ctx.BlockMatrixCache += id -> bm.persist(storageLevel)
 
   def loweredTyp: Type = TVoid
 }

hail/src/main/scala/is/hail/utils/ErrorHandling.scala

@@ -18,7 +18,7 @@ class HailWorkerException(
 trait ErrorHandling {
   def fatal(msg: String): Nothing = throw new HailException(msg)
 
-  def fatal(msg: String, errorId: Int) = throw new HailException(msg, errorId)
+  def fatal(msg: String, errorId: Int): Nothing = throw new HailException(msg, errorId)
 
   def fatal(msg: String, cause: Throwable): Nothing = throw new HailException(msg, None, cause)
 

hail/src/main/scala/is/hail/utils/ImmutableMap.scala

@@ -0,0 +1,25 @@
+package is.hail.utils
+
+import scala.collection.mutable
+
+case class ImmutableMap[K, V](m: Map[K, V]) extends mutable.AbstractMap[K, V] {
+  override def +=(kv: (K, V)): ImmutableMap.this.type =
+    throw new UnsupportedOperationException()
+
+  override def -=(key: K): ImmutableMap.this.type =
+    throw new UnsupportedOperationException()
+
+  override def get(key: K): Option[V] =
+    m.get(key)
+
+  override def iterator: Iterator[(K, V)] =
+    m.iterator
+
+  override def toMap[T, U](implicit ev: (K, V) <:< (T, U)): Map[T, U] =
+    m.toMap
+}
+
+object ImmutableMap {
+  def empty[K, V]: ImmutableMap[K, V] =
+    ImmutableMap(Map.empty)
+}

hail/src/main/scala/is/hail/utils/richUtils/RichMap.scala

@@ -1,5 +1,9 @@
 package is.hail.utils.richUtils
 
+import is.hail.utils.ImmutableMap
+
+import scala.collection.mutable
+
 class RichMap[K, V](val m: Map[K, V]) extends AnyVal {
   def force =
     m.map(identity) // needed to make serializable: https://issues.scala-lang.org/browse/SI-7005
@@ -9,4 +13,7 @@ class RichMap[K, V](val m: Map[K, V]) extends AnyVal {
 
   def isTrivial(implicit eq: K =:= V): Boolean =
     m.forall { case (k, v) => k == v }
+
+  def immutableMutableMap: mutable.Map[K, V] =
+    ImmutableMap(m)
 }